GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Klebsiella michiganensis M5al

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate BWI76_RS27555 BWI76_RS27555 putative sugar kinase/transcriptional regulator, ATPase domain protein

Query= reanno::SB2B:6937235
         (310 letters)



>FitnessBrowser__Koxy:BWI76_RS27555
          Length = 310

 Score =  225 bits (573), Expect = 1e-63
 Identities = 127/296 (42%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 5   GIDLGGTKIELVTLNEKGEEVFRKRVPTPKDYR----ATLEAVAGLVHDSEKETGQVSSV 60
           G+D+GG+KI  V ++E+G E  R RV T K  R    ATL  +   + D   E  Q  ++
Sbjct: 5   GLDIGGSKIAAVVMDEQGHEWRRFRVETRKQTRQQFIATLVELITAIGD---ELAQPLAI 61

Query: 61  GIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGA 120
           GI +PG +S  +G+++N+N   +NG  +  +L   LG+ V +AND NCFA+SE+ DG GA
Sbjct: 62  GIALPGSISPQSGKIRNANIQVINGCRLQDELEQRLGQSVVLANDGNCFALSEACDGAGA 121

Query: 121 GKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLP-WMTADEFNSTRCFCGNAD 179
             +LVFG  LGTGCG GIA+N ++  G +GI  E GH  LP +   ++    RC+CG  +
Sbjct: 122 DYSLVFGMTLGTGCGGGIALNRQIFPGASGIAAECGHITLPGYQEVNDGPPARCYCGKYN 181

Query: 180 CIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINL 239
           C+E+F+SGTG    +R    EA S   I+A   +GE  A     RF  +LAR LA V+NL
Sbjct: 182 CVESFISGTGLSARYRLLTQEALSSQAIIARALEGEHAACEQVLRFRQQLARTLATVVNL 241

Query: 240 LDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295
           +DP VI+LGGG+SN+  +   L A +   V      T +V   HG SSG+RGAAWL
Sbjct: 242 IDPGVIILGGGLSNVALLVNDLEADVAPLVFTDHFITPIVPARHGDSSGMRGAAWL 297


Lambda     K      H
   0.318    0.138    0.424 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 291
Number of extensions: 12
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory